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Guide to finding & buying low-toxicity building caulk or sealant products:
This article describes non-toxic caulks & sealants used in buildings, aquariums, water cisterns or springs and similar applications.
We answer a reader question about how to seal a leaky water container for a spring, and we list several low-toxicity caulk brands for which we include key properties (and in some cases warnings) from the caulk MSDS data.
Guide to Choosing & Buying Non-Toxic or Low Toxicity Caulks & Sealants
Question: what to use to patch a leaky springwater container
I have a hand dug and stone and cement spring at my camp which isn't holding water very well.
I want to patch the inside with something that can stay wet and won't be toxic, any ideas?
- D.H. 4/3/2013
Reply: approaches to sealing a spring or other container intended to contain potable water
Below we describe several products that may be suitable and successful in making a patch to a leak for a concrete (or other) container that is used to hold drinking water.
But before advising patching I'd need to understand how your water system is constructed. When I was a kid our spring-fed water supply entered up through sandy soil in the bottom of a spring-fed springhouse that was surrounded by concrete and covered with a roof.
[Click any InspectApedia.com image to see an enlarged detailed version.]
We tossed our watermelons in there to stay cold during the summer. But if the spring water level in that design dropped it wasn't a leak in the springhouse it was a drop in the groundwater levels.
Watch out: at SPRINGS as WATER SUPPLY we describe other more broad concerns with the safety of cisterns and springs as drinking water sources.
Hydraulic cement, high in portland content, is compatible and as it's essentially the same as what you've already got - concrete - about the same in toxicity. But if the cracks and leaks are because the concrete structure you built to contain springwater is tipping, bending, breaking, leaks will probably recur until you fix the underlying support.
Since we include warnings in MSDS sheets for the other sealants discussed below I note that while cured cement has been used for centuries as a successful and low-toxicity container for water in cisterns and springwater enclosures, cement or concrete can be highly toxic and caustic during construction or repair.
Aquarium sealant: an alternative that is surely not toxic would be to try a silicone or similar sealant sold for use in constructing an aquarium.
If we have a product that doesn't kill the fish that's a good sign.
As you will see from our clip of advertisements for aquarium sealers in our photo above these are generally silicone sealant products sold by Ag, DAP, DOW, Marineland, Perfecto, and other manufacturers.
Swimming pool or marine product (boat) sealants: An alternative for which you'd need to read the MSDS but that might work well would be swimming pool patching compounds. We list some approaches to sealing swimming pool leaks in our resources list below, including Atlas Pool Putty and Fix-A-Leak that may have special application depending on where the leak is located.
I am hesitant to recommend caulks and sealants in generic form - one should first check the caulk's ingredients, solvents, and chemistry. But in general, the most toxic chemical in some caulks would be mineral spirits (possibly a source of benzene, a carcinogen, for example). Acrylic / latex caulks, do not contain mineral spirits.
Silicone or acrylic compounds in caulks and sealants are key ingredients in forming their waterproof properties when cured.
Watch out: the Mother Earth Living website contributor Debra Lynn Dodd (author of Home Safe Home ) recommended three caulks as "non toxic" that I list below.
However a look at the product MSDS sheets is further informative so I include some excerpts, noting that the possible toxicity of caulks, sealants, and coatings may be quite different between when the product is opened and applied and when it has cured, as VOCs and other products diminish during the curing and drying process.
Certainly in the various caulk & sealant MSDS data sheets it is apparent that the risks discussed focus on exposure to the product "out of the box" or container, that is, before it has been applied, cured, diluted, etc.
List of Non-Toxic or Low-toxicity Caulks & Sealants
Dap Acrylic Caulk - http://www.dap.com - MSDS cites ethylene glycol, an automotive type antifreeze, and formaldehyde in the MSDS for Alex Plus Clear Latex Caulk.
From the product MSDS:
Emergency Overview: A white to off-white paste product with a very slight ammonia odor. WARNING! May cause eye,
skin, nose, throat and respiratory tract irritation. May cause eye or skin irritation. Harmful if swallowed or absorbed through
the skin. This product contains ethylene glycol.
The MSDS Section 11 - Toxicological Information notes the following:
Significant Data with Possible Relevance to Humans: This product contains trace amounts of free formaldehyde.
OSHA and NTP identify formaldehyde as a potential carcinogen. IARC identifies formaldehyde as a human carcinogen.
Formaldehyde has been shown to cause mutations in a variety of in-vitro test systems, the significance of which to
humans is unknown. There should be minimal risk when used with ventilation adequate to keep the atmospheric
concentration of formaldehyde below the recommended exposure limits.
Maintain adequate ventilation to prevent exposure above current OSHA / ACGIH exposure limits. Workplace monitoring of
the air to define formaldehyde exposure levels may be necessary.
In a two-year inhalation study, rats showed carcinogenic effects in the respiratory system at 15 ppm of formaldehyde.
Section 12 provides this statement: Ecological Information: Ecological injuries are not known or expected under normal use.
Dow Corning 100% Silicone Sealant - http://www.dowcorning.com - (Watch out: the company has so many products lines and products that you will have to navigate a forest of web pages often ending at a dead-end)
The Dow MSDS for Dow Corning® 790 Silicone Building Sealant, Gray, MSDS section on Potential Health Effects from acute exposure includes warnings for Eye: Direct contact may cause severe irritation, Skin: May cause moderate irritation, Inhalation: Irritates respiratory passages very slightly, and Oral: Low ingestion hazard in normal use. Effects are different in cases of prolonged or repeated exposure.
The Dow Corning Silicone Sealant
MSDS Section 11 states: Contains Bis(N-methyl acetamido)silane which liberates N-methylacetamide (NMA) during cure. NMA has been shown
to cause birth defects in laboratory animals.
Section 12 Ecological Information states "Complete information is not yet available."
Safecoat Caulking Compound (modified acrylic polymer) - http://www.afmsafecoat.com - describes this product as Safecoat Caulking Compound is a not-toxic, elastic emulsion type caulking compound designed to replace oil caulk and putty for windows, cracks and general maintenance work. 
Significantly the MSDS states
Section 311/312 Categorizations (40 CFR 370): Not a hazardous chemical
Section 313 Information (40 CFR 372): This product does not contain a chemical
which is listed in Section 313 above de minimis concentrations.
The Safecoat Caulking Compound MSDS for Safecoat 7130 White, does not contain a Section 11 on Toxicology nor a Section12 on Environmental impact.
The product contains Propylene Glycol (for which the acute oral toxicity is stated by sources such as Wikipedia as "very low"), Titanium Dioxide (used in sunscreens, possibly toxic in sunscreens  and separately, especially in dust form), and of course other materials. Hazards would occur principally from swallowing or inhalation of the product. 
Other Caulks or Sealants for Pools & Water-Containers
Atlas Epoxy Bond Pool Putty, Atlas Mineral & Chemicals, Inc is a two part resin and hardener epoxy repair product that can be used to seal holes or cracks in swimming pools and capable of working under water provided the surfaces have been cleaned of slime and algae or loose particles and debris. This product is specifically formulated for use on concrete or Gunnite swimming pools.
Watch out: the product data sheet (www.atlasmin.com/products/epoxybond/pdf/5-61pi--6-06.pdf) is not in our OPINION a valid MSDS and takes care to include this warning:
The materials referred to in this Data Sheet present
handling and potential health hazards. Consult Material
Safety Data Sheets and the container labels for
complete precautionary information.
We did eventually find an MSDS for this product that identifies its potential hazards as:
Routes of Entry: Inhalation: YES Skin:NO Ingestion:NO
Reports of Carcinogenicity: NTP:YES IARC:YES OSHA:NO
Health Hazards Acute and Chronic: EYES: MAY CAUSE IRRITATION. SKIN: MAY
CAUSE IRRITATION & SENSITIZATION.
Effects of Overexposure:IRRITATION.
Medical Cond Aggravated by Exposure:RESPIRATORY PROBLEMS, ALLERGIES,
Fix-A-Leak [swimming pool sealant], Marlig Industries, Niagara Falls, Ontario. is a product that is poured into the pool plumbing system, circulates through the system and in theory flows to and fixes leak points.
This product might be tempting to use if the leak in a spring-fed or cistern-fed water supply system has not been pinpointed but we need to be convinced that the compound is harmless in drinking water and that it will find, seep into, and repair a leak in a cistern type structure. The Fix-a-Leak Pool Sealant MSDS includes this summary statement:
Hazard Identification: This product is classified as a hazardous substance and as dangerous goods according to the classification criteria of NOHSC and
ADG Code (Australia). Warning! Contents under pressure! Highly flammable liquid and vapor! Vapor may cause flash fire! Keep away from heat,
sparks, and open flames.
Do not puncture or incinerate. Do not store above 130°F. Use only with adequate ventilation. Keep containers closed when not
in use. Keep away from children.
Routes of Entry: Inhalation, Skin & Eyes, Ingestion 
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